Abundance and diversity of endogenous retroviruses in the chicken genome

Long terminal repeat (LTR) retrotransposons are autonomous eukaryotic repetitive elements which may elicit prolonged genomic and immunological stress on their host organism. LTR retrotransposons comprise approximately 10 % of the mammalian genome, but previous work identified only 1.35 % of the chicken genome as LTR retrotransposon sequence. This deficit appears inconsistent across birds, as studied Neoaves have contents comparable with mammals, although all birds contain only one LTR retrotransposon class: endogenous retroviruses (ERVs). One group of chicken-specific ERVs (Avian Leukosis Virus subgroup E; ALVEs) remain active and have been linked to commercially detrimental phenotypes, such as reduced lifetime egg count, but their full diversity and range of phenotypic effects are poorly understood. A novel identification pipeline, LocaTR, was developed to identify LTR retrotransposon sequences in the chicken genome. This enabled the annotation of 3.01 % of the genome, including 1,073 structurally intact elements with replicative potential. Elements were depleted within coding regions, and over 40 % of intact elements were found in clusters in gene sparse, poorly recombining regions. RNAseq analysis showed that elements were generally not expressed, but intact transcripts were identified in four cases, supporting the potential for viral recombination and retrotransposition of non-autonomous repeats. LocaTR analysis of seventy-two additional sauropsid genomes revealed highly lineage-specific repeat content, and did not support the proposed deficit in Galliformes. A second, novel bioinformatic pipeline was constructed to identify ALVE insertions in whole genome resequencing data and was applied to eight elite layer lines from Hy-Line International. Twenty ALVEs were identified and diagnostic assays were developed to validate the bioinformatic approach. Each ALVE was sequenced and characterised, with many exhibiting high structural intactness. In addition, a K locus revertant line was identified due to the unexpected presence of ALVE21, confirmed using BioNano optic maps. The ALVE identification pipeline was then applied to ninety chicken lines and 322 different ALVEs were identified, 81 % of which were novel. Overall, broilers and non-commercial chickens had a greater number of ALVEs than were found in layers. Taken together, these two analyses have enabled a thorough characterisation of both the abundance and diversity of chicken ERVs

MendelianRandomization v0.5.0: updates to an R package for performing Mendelian randomization analyses using summarized data.

The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added to the package or updated in recent years. These features can be divided into four categories: robust methods for Mendelian randomization, methods for multivariable Mendelian randomization, functions for data visualization, and the ability to load data into the package seamlessly from the PhenoScanner web-resource. We provide examples of the graphical output produced by the data visualization commands, as well as syntax for obtaining suitable data and performing a Mendelian randomization analysis in a single line of code

Use of a Non-Penetrating Captive Bolt for Euthanasia of Neonate Goats

A non-penetrating captive bolt device, powered by a 1 grain 0.22″ cartridge delivering a calculated kinetic energy of 47 Joules was tested as a euthanasia method on 200 neonate goats (Capra aegagrus hircus) of mean dead weight = 4.425 kg (SD (Standard deviation) ± 0.4632), to assess effectiveness and shot position. Evaluation of the method was conducted using behavioural indicators of brain dysfunction followed by post mortem examination of the heads. Once correct shot position had been established, 100% of 158 kids (95% confidence interval 97.5% to 100%) were successfully stunned/killed with a shot positioned on the midline, between the ears, with the chin tucked into the neck. The use of the Accles and Shelvoke CASH Small Animal Tool can therefore be recommended for the euthanasia of neonate goats with a 1 grain cartridge and a specific shooting position

The Use of a Non-Penetrating Captive Bolt for the Euthanasia of Neonate Piglets

The most common method for the on-farm euthanasia of neonate piglets is reported to be manual blunt force trauma. This paper presents the results of research to evaluate a mechanical non-penetrating captive bolt (the Accles and Shelvoke CASH small animal tool, Birmingham, UK) to produce an immediate stun/kill with neonate piglets. One hundred and forty-seven piglets (average dead weight = 1.20 kg ± 0.58 (standard deviation, SD), mean age = 5.8 days (median = 3)) were euthanized with the device and demonstrated immediate loss of consciousness, subjectively assessed by behavioural signs and no recovery. The result that 147 out of 147 animals were effectively stun/killed gives a 95% confidence interval for the true percentage of animals that would be effectively stun/killed of 97.5–100% with the use of the CASH small animal tool under the conditions of the current study. This research concludes that the CASH small animal tool, using a 1 grain brown coded cartridge, is suitable for producing a stun/kill in neonate piglets when applied in a frontal/parietal position

The Use of a Mechanical Non-Penetrating Captive Bolt Device for the Euthanasia of Neonate Lambs

A non-penetrating captive bolt device, powered by a 1-grain 0.22″ cartridge delivering a calculated kinetic energy of 47 Joules was tested as a euthanasia method on 200 neonate lambs (Ovis aries) of 4.464 kg (SD (Standard deviation) ± 1.056) mean dead weight, to assess effectiveness and shot position. Every lamb (n = 200) was effectively stunned when the weapon was applied powered by a brown, 1-grain cartridge but 10/200 (5%) of the lambs displayed rhythmic or agonal breathing and were subsequently euthanased using euthatal (Merial, UK, GTIN: 03661103015550). Evaluation of the method was conducted using behavioural indicators of brain dysfunction followed by post-mortem examination of the heads. A second trial was conducted using a higher velocity 1.25-grain cartridge and a specific shot position on 48 lambs (mean dead weight = 6.21 kg, SD ± 1.24) averaging 5 days old. One hundred percent of the lambs in the second trial were immediately stun-killed. Given this complete kill rate and the sample size of the study, the study provides a statistical 95% confidence interval of 92.6% to 100%. The use of the Accles & Shelvoke “CASH” Small Animal Tool (Birmingham, UK) can therefore be recommended for the euthanasia of neonate lambs with a 1.25-grain cartridge and a specific shooting position

Overlapping functions of the cell adhesion molecules Nr-CAM and L1 in cerebellar granule cell development

The structurally related cell adhesion molecules L1 and Nr-CAM have overlapping expression patterns in cerebellar granule cells. Here we analyzed their involvement in granule cell development using mutant mice. Nr-CAM–deficient cerebellar granule cells failed to extend neurites in vitro on contactin, a known ligand for Nr-CAM expressed in the cerebellum, confirming that these mice are functionally null for Nr-CAM. In vivo, Nr-CAM–null cerebella did not exhibit obvious histological defects, although a mild size reduction of several lobes was observed, most notably lobes IV and V in the vermis. Mice deficient for both L1 and Nr-CAM exhibited severe cerebellar folial defects and a reduction in the thickness of the inner granule cell layer. Additionally, anti-L1 antibodies specifically disrupted survival and maintenance of Nr-CAM–deficient granule cells in cerebellar cultures treated with antibodies. The combined results indicate that Nr-CAM and L1 play a role in cerebellar granule cell development, and suggest that closely related molecules in the L1 family have overlapping functions

Breast cancer dependence on MCL-1 is due to its canonical anti-apoptotic function-AAM

High levels of the anti-apoptotic BCL-2 family member MCL-1 are frequently found in breast cancer and, appropriately, BH3-mimetic drugs that specifically target MCL-1’s function in apoptosis are in development as anti-cancer therapy. MCL-1 also has reported non-canonical roles that may be relevant in its tumour-promoting effect. Here we investigate the role of MCL-1 in clinically relevant breast cancer models and address whether the canonical role of MCL-1 in apoptosis, which can be targeted using BH3-mimetic drugs, is the major function for MCL-1 in breast cancer. We show that MCL-1 is essential in established tumours with genetic deletion inducing tumour regression and inhibition with the MCL-1-specific BH3-mimetic drug S63845 significantly impeding tumour growth. Importantly, we found that the anti-tumour functions achieved by MCL-1 deletion or inhibition were completely dependent on pro-apoptotic BAX/BAK. Interestingly, we find that MCL-1 is also critical for stem cell activity in human breast cancer cells and high MCL1 expression correlates with stemness markers in tumours. This strongly supports the idea that the key function of MCL-1 in breast cancer is through its anti-apoptotic function. This has important implications for the future use of MCL-1-specific BH3-mimetic drugs in breast cancer treatment

Mixed methods evaluation of the Getting it Right First Time programme in elective orthopaedic surgery in England: an analysis from the National Joint Registry and Hospital Episode Statistics

OBJECTIVE: To evaluate the impact of the 'Getting it Right First Time' (GIRFT) national improvement programme in orthopaedics, which started in 2012. DESIGN: Mixed-methods study comprising statistical analysis of linked national datasets (National Joint Registry; Hospital Episode Statistics; Patient-Reported Outcomes); economic analysis and qualitative case studies in six National Health Service (NHS) Trusts. SETTING: NHS elective orthopaedic surgery in England. PARTICIPANTS: 736 088 patients who underwent primary hip or knee replacement at 126 NHS Trusts between 1 April 2009 and 31 March 2018, plus 50 NHS staff. INTERVENTION: Improvement bundle including 'deep dive' visits by senior clinician to NHS Trusts, informed by bespoke set of routine performance data, to discuss how improvements could be made locally. MAIN OUTCOME MEASURES: Number of procedures conducted by low volume surgeons; use of uncemented hip implants in patients >65; arthroscopy in year prior to knee replacement; hospital length of stay; emergency readmissions within 30 days; revision surgery within 1 year; health-related quality of life and functional status. RESULTS: National trends demonstrated substantial improvements beginning prior to GIRFT. Between 2012 and 2018, there were reductions in procedures by low volume surgeons (ORs (95% CI) hips 0.58 (0.53 to 0.63), knees 0.77 (0.72 to 0.83)); uncemented hip prostheses in >65 s (OR 0.56 (0.51 to 0.61)); knee arthroscopies before surgery (OR 0.48 (0.41 to 0.56)) and mean length of stay (hips -0.90 (-1.00 to -0.81), knees -0.74 days (-0.82 to -0.66)). The additional impact of visits was mixed and comprised an overall economic saving of £431 848 between 2012 and 2018, but this was offset by the costs of the visits. Staff reported that GIRFT's influence ranged from procurement changes to improved regional collaboration. CONCLUSION: Nationally, we found substantial improvements in care, but the specific contribution of GIRFT cannot be reliably estimated due to other concurrent initiatives. Our approach enabled additional analysis of the discrete impact of GIRFT visits